library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)
load(file = "Leukemia_curated.rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS
## 0.000000001
## HADDAD_B_LYMPHOCYTE_PROGENITOR
## 0.000000001
## SMID_BREAST_CANCER_LUMINAL_B_DN
## 0.000000001
## SMID_BREAST_CANCER_NORMAL_LIKE_UP
## 0.000000001
## SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12
## 0.000000001
## ROME_INSULIN_TARGETS_IN_MUSCLE_DN
## 0.000000001
## POOLA_INVASIVE_BREAST_CANCER_UP
## 0.000000001
## RAO_BOUND_BY_SALL4
## 0.000000001
## REACTOME_ADAPTIVE_IMMUNE_SYSTEM
## 0.001000001
## YAGI_AML_WITH_11Q23_REARRANGED
## 0.001000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 186
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 8
nominal_dcor_q_values_under_25
## REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS
## 4.19e-07
## HADDAD_B_LYMPHOCYTE_PROGENITOR
## 4.19e-07
## SMID_BREAST_CANCER_LUMINAL_B_DN
## 4.19e-07
## SMID_BREAST_CANCER_NORMAL_LIKE_UP
## 4.19e-07
## SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12
## 4.19e-07
## ROME_INSULIN_TARGETS_IN_MUSCLE_DN
## 4.19e-07
## POOLA_INVASIVE_BREAST_CANCER_UP
## 4.19e-07
## RAO_BOUND_BY_SALL4
## 4.19e-07
nrow(gsea_results_significant)
## [1] 335
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 121
Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))
Mutually_identified_in_GSEA_dcor
## [1] "HADDAD_B_LYMPHOCYTE_PROGENITOR"
## [2] "RAO_BOUND_BY_SALL4"
## [3] "REACTOME_ADAPTIVE_IMMUNE_SYSTEM"
## [4] "REACTOME_GPCR_LIGAND_BINDING"
## [5] "GOLUB_ALL_VS_AML_UP"
## [6] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"
## [7] "KLEIN_TARGETS_OF_BCR_ABL1_FUSION"
## [8] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [9] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"
## [10] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"
## [11] "BIOCARTA_CTCF_PATHWAY"
## [12] "HUMMEL_BURKITTS_LYMPHOMA_UP"
## [13] "WANG_CLIM2_TARGETS_DN"
## [14] "VALK_AML_CLUSTER_1"
## [15] "SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES"
## [16] "BROWN_MYELOID_CELL_DEVELOPMENT_UP"
## [17] "KEGG_PRIMARY_IMMUNODEFICIENCY"
## [18] "REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR"
## [19] "HOLLMANN_APOPTOSIS_VIA_CD40_DN"
## [20] "RIZKI_TUMOR_INVASIVENESS_2D_UP"
## [21] "SIG_BCR_SIGNALING_PATHWAY"
## [22] "BHAT_ESR1_TARGETS_VIA_AKT1_DN"
## [23] "HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP"
## [24] "PROVENZANI_METASTASIS_UP"
## [25] "PARK_HSC_AND_MULTIPOTENT_PROGENITORS"
## [26] "HOSHIDA_LIVER_CANCER_SURVIVAL_UP"
## [27] "SESTO_RESPONSE_TO_UV_C5"
## [28] "BAELDE_DIABETIC_NEPHROPATHY_DN"
## [29] "BASSO_CD40_SIGNALING_DN"
## [30] "PID_BETA_CATENIN_NUC_PATHWAY"
## [31] "LEE_RECENT_THYMIC_EMIGRANT"
## [32] "LABBE_WNT3A_TARGETS_UP"
## [33] "BAKKER_FOXO3_TARGETS_DN"
## [34] "PID_BCR_5PATHWAY"
## [35] "ONKEN_UVEAL_MELANOMA_UP"
## [36] "BOYLAN_MULTIPLE_MYELOMA_PCA3_DN"
## [37] "ZHAN_MULTIPLE_MYELOMA_PR_DN"
## [38] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"
## [39] "CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE"
## [40] "NOUZOVA_TRETINOIN_AND_H4_ACETYLATION"
## [41] "ST_B_CELL_ANTIGEN_RECEPTOR"
## [42] "BILANGES_SERUM_SENSITIVE_VIA_TSC2"
## [43] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP"
## [44] "GRADE_METASTASIS_DN"
## [45] "REACTOME_PI_METABOLISM"
## [46] "CROMER_METASTASIS_UP"
## [47] "LEE_LIVER_CANCER_E2F1_UP"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 1
Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS | SMID_BREAST_CANCER_LUMINAL_B_DN | SMID_BREAST_CANCER_NORMAL_LIKE_UP | SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 | ROME_INSULIN_TARGETS_IN_MUSCLE_DN | POOLA_INVASIVE_BREAST_CANCER_UP | YAGI_AML_WITH_11Q23_REARRANGED | DELACROIX_RAR_BOUND_ES | SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN | TSENG_ADIPOGENIC_POTENTIAL_UP | BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B | PASINI_SUZ12_TARGETS_UP | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP | AMIT_SERUM_RESPONSE_480_MCF10A | ROY_WOUND_BLOOD_VESSEL_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP | AIGNER_ZEB1_TARGETS | COATES_MACROPHAGE_M1_VS_M2_DN | GRADE_COLON_VS_RECTAL_CANCER_DN | REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | JI_METASTASIS_REPRESSED_BY_STK11 | RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN | ABBUD_LIF_SIGNALING_1_DN | KUMAR_TARGETS_OF_MLL_AF9_FUSION | IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM | XU_GH1_AUTOCRINE_TARGETS_UP | HOELZEL_NF1_TARGETS_DN | MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN | VANTVEER_BREAST_CANCER_BRCA1_UP | WENDT_COHESIN_TARGETS_UP | INGRAM_SHH_TARGETS_DN | FERRANDO_HOX11_NEIGHBORS | CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY | JAEGER_METASTASIS_UP | SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP | BURTON_ADIPOGENESIS_11 | HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP | LABBE_WNT3A_TARGETS_DN | DE_YY1_TARGETS_DN | BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING | MIKKELSEN_ES_ICP_WITH_H3K4ME3 | DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN | HOLLERN_EMT_BREAST_TUMOR_DN | REACTOME_G_ALPHA_I_SIGNALLING_EVENTS | MANN_RESPONSE_TO_AMIFOSTINE_UP | DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 | HECKER_IFNB1_TARGETS | SANSOM_APC_TARGETS_DN | SIMBULAN_PARP1_TARGETS_DN | RIGGI_EWING_SARCOMA_PROGENITOR_DN | REACTOME_L1CAM_INTERACTIONS | LIU_SOX4_TARGETS_UP | NEWMAN_ERCC6_TARGETS_UP | MAHADEVAN_IMATINIB_RESISTANCE_DN | PETRETTO_CARDIAC_HYPERTROPHY | BOCHKIS_FOXA2_TARGETS | CHANG_IMMORTALIZED_BY_HPV31_UP | ONO_FOXP3_TARGETS_DN | PENG_RAPAMYCIN_RESPONSE_UP | ZHAN_MULTIPLE_MYELOMA_CD2_UP | SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN | KAMMINGA_SENESCENCE | DELLA_RESPONSE_TO_TSA_AND_BUTYRATE | PLASARI_TGFB1_TARGETS_10HR_DN | BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN | SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY | WIELAND_UP_BY_HBV_INFECTION | WONG_IFNA2_RESISTANCE_DN | GRESHOCK_CANCER_COPY_NUMBER_UP | YANG_BREAST_CANCER_ESR1_LASER_DN | VECCHI_GASTRIC_CANCER_EARLY_DN | WOO_LIVER_CANCER_RECURRENCE_UP | REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE | HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP | ONO_AML1_TARGETS_DN | WNT_SIGNALING | LIU_VAV3_PROSTATE_CARCINOGENESIS_UP | BAUS_TFF2_TARGETS_UP | REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES | BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP | CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN | BURTON_ADIPOGENESIS_7 | DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN | GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN | BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP | MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 | TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN | MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN | DANG_MYC_TARGETS_DN | XU_CREBBP_TARGETS_DN | MARSON_FOXP3_TARGETS_STIMULATED_UP | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN | HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP | ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP | YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 | ALFANO_MYC_TARGETS | REACTOME_REGULATION_OF_SIGNALING_BY_CBL | SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN | IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN | VERHAAK_AML_WITH_NPM1_MUTATED_DN | ISSAEVA_MLL2_TARGETS | BROWNE_HCMV_INFECTION_48HR_UP | REACTOME_GPCR_DOWNSTREAM_SIGNALING | SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN | DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP | QI_PLASMACYTOMA_UP | GAVIN_FOXP3_TARGETS_CLUSTER_P2 | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP | RIZKI_TUMOR_INVASIVENESS_3D_UP | FUJII_YBX1_TARGETS_DN | ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP | CHENG_RESPONSE_TO_NICKEL_ACETATE | ZHENG_FOXP3_TARGETS_IN_THYMUS_UP | NUTT_GBM_VS_AO_GLIOMA_UP | MORI_LARGE_PRE_BII_LYMPHOCYTE_DN | YAMAZAKI_TCEB3_TARGETS_DN | KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 | KEGG_PROTEASOME | REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES | LIAO_HAVE_SOX4_BINDING_SITES | SMIRNOV_RESPONSE_TO_IR_6HR_DN | REACTOME_NEPHRIN_INTERACTIONS | REACTOME_CHOLESTEROL_BIOSYNTHESIS | NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN | OUYANG_PROSTATE_CANCER_PROGRESSION_DN | THILLAINADESAN_ZNF217_TARGETS_UP | PID_HES_HEY_PATHWAY | ONDER_CDH1_TARGETS_2_UP | BROWNE_HCMV_INFECTION_1HR_DN | LEE_LIVER_CANCER_DENA_UP | AMIT_SERUM_RESPONSE_240_MCF10A | LU_TUMOR_ANGIOGENESIS_UP | EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION | BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN | ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN | BIOCARTA_PROTEASOME_PATHWAY | REACTOME_DEVELOPMENTAL_BIOLOGY | REACTOME_MYOGENESIS | CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0010 | 0.0010 | 0.0020 | 0.0020 | 0.0020 | 0.0020 | 0.0030 | 0.0030 | 0.0040 | 0.0040 | 0.0040 | 0.004 | 0.0040 | 0.0050 | 0.005 | 0.0050 | 0.0060 | 0.0060 | 0.0060 | 0.006 | 0.0060 | 0.0070 | 0.0070 | 0.0070 | 0.0080 | 0.0080 | 0.0080 | 0.0090 | 0.0090 | 0.0090 | 0.0090 | 0.0090 | 0.0100 | 0.0100 | 0.0100 | 0.0100 | 0.0100 | 0.0110 | 0.0120 | 0.0120 | 0.0120 | 0.0130 | 0.0130 | 0.0140 | 0.0150 | 0.0150 | 0.0150 | 0.0150 | 0.0150 | 0.0150 | 0.0160 | 0.0160 | 0.0170 | 0.017 | 0.0170 | 0.0170 | 0.0190 | 0.019 | 0.0200 | 0.0210 | 0.0210 | 0.021 | 0.0210 | 0.0220 | 0.0230 | 0.0230 | 0.0240 | 0.0240 | 0.024 | 0.0250 | 0.0250 | 0.025 | 0.0260 | 0.0260 | 0.0280 | 0.0280 | 0.0280 | 0.0290 | 0.0290 | 0.0290 | 0.0290 | 0.0300 | 0.0300 | 0.0310 | 0.0310 | 0.0320 | 0.0320 | 0.032 | 0.032 | 0.032 | 0.0330 | 0.0330 | 0.033 | 0.0330 | 0.0340 | 0.0350 | 0.0360 | 0.0360 | 0.0360 | 0.0360 | 0.0370 | 0.0380 | 0.0380 | 0.0380 | 0.0380 | 0.0390 | 0.0390 | 0.0390 | 0.0400 | 0.0400 | 0.0400 | 0.0410 | 0.0410 | 0.0410 | 0.0410 | 0.042 | 0.0420 | 0.0420 | 0.0420 | 0.042 | 0.0430 | 0.0430 | 0.0430 | 0.0450 | 0.0460 | 0.0470 | 0.0480 | 0.0480 | 0.0480 | 0.0490 | 0.049 | 0.0490 | 0.0490 |
| GSEA | 0.0682 | 0.5029 | 0.1841 | 0.5105 | 0.3888 | 0.4875 | 0.0702 | 0.1395 | 0.5824 | 0.3188 | 0.3256 | 0.0672 | 0.8162 | 0.1279 | 0.5845 | 0.3265 | 0.4809 | 0.300 | 0.5645 | 0.0564 | 0.192 | 0.7079 | 0.1633 | 0.1954 | 0.0529 | 0.298 | 0.3519 | 0.4853 | 0.1065 | 0.0637 | 0.2769 | 0.0564 | 0.0691 | 0.3683 | 0.9006 | 0.0651 | 0.2031 | 0.5168 | 0.2147 | 0.7449 | 0.6163 | 0.1916 | 0.9075 | 0.1561 | 0.5238 | 0.3961 | 0.6047 | 0.1734 | 0.3727 | 0.6667 | 0.6263 | 0.0602 | 0.2739 | 0.3295 | 0.7196 | 0.3613 | 0.5835 | 0.2275 | 0.1085 | 0.217 | 0.3451 | 0.1755 | 0.1731 | 0.524 | 0.5156 | 0.6918 | 0.1453 | 0.284 | 0.0885 | 0.1837 | 0.4693 | 0.4962 | 0.0861 | 0.2344 | 0.072 | 0.4738 | 0.4482 | 0.081 | 0.1042 | 0.2643 | 0.1345 | 0.3477 | 0.1744 | 0.1303 | 0.1896 | 0.2605 | 0.2812 | 0.3168 | 0.2945 | 0.2589 | 0.8472 | 0.5068 | 0.4462 | 0.176 | 0.264 | 0.578 | 0.4766 | 0.7152 | 0.753 | 0.1695 | 0.4442 | 0.2675 | 0.3023 | 0.5703 | 0.4118 | 0.1319 | 0.2308 | 0.1184 | 0.2994 | 0.1085 | 0.2378 | 0.4347 | 0.0606 | 0.1238 | 0.5494 | 0.1111 | 0.7425 | 0.0664 | 0.0916 | 0.2927 | 0.0549 | 0.072 | 0.1107 | 0.0668 | 0.3773 | 0.083 | 0.1835 | 0.8323 | 0.2238 | 0.1016 | 0.2879 | 0.2337 | 0.7992 | 0.1384 | 0.4139 | 0.1205 | 0.739 | 0.2089 | 0.6854 |
Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
kable("html", digits = 4, longtable = TRUE) %>%
kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
row_spec(0, angle = -0)
| BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN | FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN | DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN | PUJANA_BRCA2_PCC_NETWORK | KEGG_BASE_EXCISION_REPAIR | REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES | REACTOME_CELL_CYCLE | GARY_CD5_TARGETS_DN | MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 | DAZARD_RESPONSE_TO_UV_NHEK_DN | BENPORATH_PROLIFERATION | NUYTTEN_EZH2_TARGETS_DN | KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY | REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP | RAMALHO_STEMNESS_UP | DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER | REACTOME_CELL_CYCLE_CHECKPOINTS | REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION | GENTILE_UV_RESPONSE_CLUSTER_D8 | MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP | REACTOME_HIV_LIFE_CYCLE | REACTOME_HIV_INFECTION | REACTOME_CHROMOSOME_MAINTENANCE | FIGUEROA_AML_METHYLATION_CLUSTER_1_DN | ZHANG_BREAST_CANCER_PROGENITORS_UP | PYEON_HPV_POSITIVE_TUMORS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN | CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP | MARSON_BOUND_BY_E2F4_UNSTIMULATED | SHEN_SMARCA2_TARGETS_UP | REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY | REACTOME_BASE_EXCISION_REPAIR | REACTOME_CELL_CYCLE_MITOTIC | REACTOME_TRANSCRIPTION | KAUFFMANN_DNA_REPAIR_GENES | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN | KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION | STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP | MITSIADES_RESPONSE_TO_APLIDIN_DN | REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS | BOYLAN_MULTIPLE_MYELOMA_C_D_UP | FEVR_CTNNB1_TARGETS_DN | REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY | REACTOME_TELOMERE_MAINTENANCE | BIDUS_METASTASIS_UP | ZHANG_TLX_TARGETS_36HR_DN | MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN | SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL | KIM_WT1_TARGETS_DN | MORI_PLASMA_CELL_DN | ENK_UV_RESPONSE_KERATINOCYTE_DN | ZHAN_EARLY_DIFFERENTIATION_GENES_DN | REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS | OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP | MATTIOLI_MGUS_VS_PCL | ABRAMSON_INTERACT_WITH_AIRE | ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP | VILLANUEVA_LIVER_CANCER_KRT19_UP | REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE | KEGG_SPLICEOSOME | MORI_MATURE_B_LYMPHOCYTE_DN | DITTMER_PTHLH_TARGETS_DN | CAIRO_HEPATOBLASTOMA_UP | BIOCARTA_BCR_PATHWAY | REACTOME_MRNA_PROCESSING | HAMAI_APOPTOSIS_VIA_TRAIL_UP | ROSS_AML_WITH_AML1_ETO_FUSION | REACTOME_GLUCOSE_TRANSPORT | REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 | REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE | PECE_MAMMARY_STEM_CELL_DN | DAZARD_UV_RESPONSE_CLUSTER_G6 | GENTILE_UV_RESPONSE_CLUSTER_D4 | REACTOME_METABOLISM_OF_NON_CODING_RNA | CHESLER_BRAIN_QTL_CIS | REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE | KAMMINGA_EZH2_TARGETS | JOHNSTONE_PARVB_TARGETS_3_DN | HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 | BROWNE_HCMV_INFECTION_10HR_DN | PEART_HDAC_PROLIFERATION_CLUSTER_UP | PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN | REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE | GALE_APL_WITH_FLT3_MUTATED_UP | REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C | HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN | HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC | BIOCARTA_CARM_ER_PATHWAY | REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION | VALK_AML_CLUSTER_10 | MILI_PSEUDOPODIA_HAPTOTAXIS_UP | BIOCARTA_PAR1_PATHWAY | SESTO_RESPONSE_TO_UV_C2 | CARD_MIR302A_TARGETS | REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 | REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 | REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION | ELLWOOD_MYC_TARGETS_DN | BENPORATH_SOX2_TARGETS | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS | BROWNE_HCMV_INFECTION_4HR_DN | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP | WAKASUGI_HAVE_ZNF143_BINDING_SITES | KIM_ALL_DISORDERS_CALB1_CORR_UP | ROESSLER_LIVER_CANCER_METASTASIS_DN | REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT | REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT | REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION | BENPORATH_ES_1 | PID_EPHA2_FWD_PATHWAY | REACTOME_RNA_POL_I_TRANSCRIPTION | YANG_BREAST_CANCER_ESR1_DN | REACTOME_MEIOSIS | REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC | BOYLAN_MULTIPLE_MYELOMA_C_UP | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT | HOLLMANN_APOPTOSIS_VIA_CD40_UP | WHITFIELD_CELL_CYCLE_G2_M | BRUINS_UVC_RESPONSE_MIDDLE | PID_P38_MK2_PATHWAY | KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP | CHENG_IMPRINTED_BY_ESTRADIOL | GAZIN_EPIGENETIC_SILENCING_BY_KRAS | RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP | TIEN_INTESTINE_PROBIOTICS_2HR_DN | ZUCCHI_METASTASIS_UP | PID_P53_REGULATION_PATHWAY | BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS | REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS | KIM_GERMINAL_CENTER_T_HELPER_UP | PID_PS1_PATHWAY | OUILLETTE_CLL_13Q14_DELETION_UP | THUM_SYSTOLIC_HEART_FAILURE_DN | REACTOME_APOPTOSIS | PID_AR_NONGENOMIC_PATHWAY | ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP | JI_RESPONSE_TO_FSH_UP | BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP | SIG_CHEMOTAXIS | BRUINS_UVC_RESPONSE_EARLY_LATE | LIN_MELANOMA_COPY_NUMBER_DN | JOHNSTONE_PARVB_TARGETS_2_DN | ACEVEDO_LIVER_CANCER_UP | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP | LAIHO_COLORECTAL_CANCER_SERRATED_DN | PID_HEDGEHOG_GLI_PATHWAY | LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q | LIN_MELANOMA_COPY_NUMBER_UP | DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP | HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP | BIOCARTA_TFF_PATHWAY | HOSHIDA_LIVER_CANCER_SUBCLASS_S2 | BENPORATH_OCT4_TARGETS | GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP | GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN | SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP | GEORGES_TARGETS_OF_MIR192_AND_MIR215 | KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN | BILD_E2F3_ONCOGENIC_SIGNATURE | LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN | WOOD_EBV_EBNA1_TARGETS_DN | BENPORATH_NANOG_TARGETS | WINTER_HYPOXIA_DN | IKEDA_MIR30_TARGETS_UP | REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK | KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD | HASLINGER_B_CLL_WITH_6Q21_DELETION | BIOCARTA_WNT_PATHWAY | YAGI_AML_WITH_T_9_11_TRANSLOCATION | HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN | BIOCARTA_CXCR4_PATHWAY | TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA | GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP | ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN | ZHAN_MULTIPLE_MYELOMA_HP_UP | REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION | MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN | VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP | BILBAN_B_CLL_LPL_UP | CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS | KEGG_NOTCH_SIGNALING_PATHWAY | HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP | LEE_CALORIE_RESTRICTION_MUSCLE_DN | KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION | KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS | KATSANOU_ELAVL1_TARGETS_DN | GYORFFY_MITOXANTRONE_RESISTANCE | MULLIGHAN_NPM1_SIGNATURE_3_DN | JIANG_TIP30_TARGETS_UP | REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS | GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN | CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 | HOFMANN_CELL_LYMPHOMA_UP | STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP | ABBUD_LIF_SIGNALING_1_UP | DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS | CHEOK_RESPONSE_TO_HD_MTX_UP | REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS | VERHAAK_AML_WITH_NPM1_MUTATED_UP | PID_INTEGRIN_CS_PATHWAY | PID_UPA_UPAR_PATHWAY | REACTOME_COLLAGEN_FORMATION | DALESSIO_TSA_RESPONSE | GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN | VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 | BIOCARTA_DC_PATHWAY | NAKAJIMA_MAST_CELL | REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE | KIM_ALL_DISORDERS_CALB1_CORR_DN | GOLUB_ALL_VS_AML_DN | PID_INTEGRIN2_PATHWAY | HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN | LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS | KRIEG_HYPOXIA_VIA_KDM3A | PID_SYNDECAN_1_PATHWAY | PARK_APL_PATHOGENESIS_DN | HWANG_PROSTATE_CANCER_MARKERS | ALONSO_METASTASIS_NEURAL_UP | AMIT_EGF_RESPONSE_120_MCF10A | LI_CISPLATIN_RESISTANCE_DN | REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL | VERRECCHIA_RESPONSE_TO_TGFB1_C2 | GROSS_ELK3_TARGETS_DN | ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION | NABA_COLLAGENS | GHANDHI_BYSTANDER_IRRADIATION_UP | KOHOUTEK_CCNT1_TARGETS | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN | KOBAYASHI_EGFR_SIGNALING_6HR_DN | REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS | SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP | REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION | MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 | VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP | KEGG_ARACHIDONIC_ACID_METABOLISM | KANG_AR_TARGETS_UP | ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP | CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP | HOLLERN_MICROACINAR_BREAST_TUMOR_UP | WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN | MIKKELSEN_MEF_ICP_WITH_H3K27ME3 | GHANDHI_DIRECT_IRRADIATION_UP | BIOCARTA_CYTOKINE_PATHWAY | MIKKELSEN_MEF_LCP_WITH_H3K27ME3 | YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP | VERRECCHIA_RESPONSE_TO_TGFB1_C1 | PID_RXR_VDR_PATHWAY | XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR | WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG | KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES | HUPER_BREAST_BASAL_VS_LUMINAL_UP | NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN | JEON_SMAD6_TARGETS_UP | PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP | PID_INTEGRIN5_PATHWAY | BIOCARTA_STEM_PATHWAY | NAKAMURA_ADIPOGENESIS_EARLY_UP | BIOCARTA_INFLAM_PATHWAY | BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP | REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS | KHETCHOUMIAN_TRIM24_TARGETS_UP | NAKAJIMA_EOSINOPHIL | SEMENZA_HIF1_TARGETS | MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP | AMIT_EGF_RESPONSE_120_HELA | YANG_MUC2_TARGETS_DUODENUM_6MO_DN | FIGUEROA_AML_METHYLATION_CLUSTER_5_DN | REACTOME_AMINE_LIGAND_BINDING_RECEPTORS | SABATES_COLORECTAL_ADENOMA_UP | PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN | SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A | MADAN_DPPA4_TARGETS | URS_ADIPOCYTE_DIFFERENTIATION_UP | ONDER_CDH1_SIGNALING_VIA_CTNNB1 | KERLEY_RESPONSE_TO_CISPLATIN_UP | CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP | MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 | LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN | SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN | MARKEY_RB1_CHRONIC_LOF_DN | SHEN_SMARCA2_TARGETS_DN | NABA_ECM_AFFILIATED | KIM_LIVER_CANCER_POOR_SURVIVAL_DN | REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS | MARTENS_TRETINOIN_RESPONSE_UP | WATANABE_COLON_CANCER_MSI_VS_MSS_UP | MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MPEA | 0.063 | 0.3520 | 0.2380 | 0.1020 | 0.103 | 0.5460 | 0.2330 | 0.589 | 0.0690 | 0.4620 | 0.3460 | 0.979 | 0.075 | 0.5030 | 0.498 | 0.5750 | 0.4350 | 0.1620 | 0.2410 | 0.0850 | 0.2470 | 0.2320 | 0.1710 | 0.2600 | 0.6520 | 0.4680 | 0.2200 | 0.6210 | 0.186 | 0.6530 | 0.781 | 0.2550 | 0.2440 | 0.3890 | 0.8080 | 0.1620 | 0.0660 | 0.1560 | 0.4520 | 0.5670 | 0.3200 | 0.6470 | 0.7230 | 0.3810 | 0.1980 | 0.8620 | 0.6280 | 0.2980 | 0.3180 | 0.3570 | 0.442 | 0.2830 | 0.1490 | 0.0920 | 0.979 | 0.1610 | 0.1560 | 0.364 | 0.8450 | 0.7380 | 0.6400 | 0.2700 | 0.5530 | 0.0770 | 0.0570 | 0.7510 | 0.1540 | 0.2420 | 0.5900 | 0.116 | 0.6600 | 0.0560 | 0.3100 | 0.2910 | 0.7930 | 0.0500 | 0.1180 | 0.0940 | 0.3520 | 0.1960 | 0.4020 | 0.2290 | 0.0890 | 0.1200 | 0.1580 | 0.0990 | 0.2960 | 0.0580 | 0.2220 | 0.3230 | 0.0680 | 0.5400 | 0.2640 | 0.2700 | 0.362 | 0.0810 | 0.0940 | 0.7630 | 0.8130 | 0.3650 | 0.2860 | 0.8410 | 0.8420 | 0.4430 | 0.5180 | 0.7900 | 0.4720 | 0.0860 | 0.894 | 0.2370 | 0.9430 | 0.695 | 0.9300 | 0.4690 | 0.0640 | 0.1880 | 0.8450 | 0.6580 | 0.8410 | 0.427 | 0.1950 | 0.4570 | 0.8120 | 0.2300 | 0.2190 | 0.3530 | 0.4460 | 0.7150 | 0.377 | 0.5520 | 0.8110 | 0.5680 | 0.3980 | 0.6640 | 0.0950 | 0.9160 | 0.804 | 0.162 | 0.6290 | 0.1110 | 0.6970 | 0.6530 | 0.1450 | 0.1180 | 0.1030 | 0.487 | 0.3380 | 0.9210 | 0.2280 | 0.3460 | 0.2260 | 0.8040 | 0.4270 | 0.7300 | 0.1390 | 0.4050 | 0.5120 | 0.9400 | 0.3500 | 0.7900 | 0.7230 | 0.0680 | 0.6600 | 0.0600 | 0.1900 | 0.1190 | 0.2790 | 0.8130 | 0.0740 | 0.2930 | 0.5540 | 0.0870 | 0.6750 | 0.9700 | 0.1670 | 0.4760 | 0.7710 | 0.1140 | 0.256 | 0.6750 | 0.7110 | 0.6640 | 0.2700 | 0.1450 | 0.0650 | 0.8650 | 0.0680 | 0.8620 | 0.2560 | 0.111 | 0.1620 | 0.3230 | 0.9190 | 0.2760 | 0.4600 | 0.485 | 0.4010 | 0.3390 | 0.669 | 0.4980 | 0.1430 | 0.321 | 0.832 | 0.1450 | 0.0540 | 0.2250 | 0.2000 | 0.0650 | 0.6910 | 0.6620 | 0.078 | 0.0570 | 0.5680 | 0.3350 | 0.9570 | 0.1750 | 0.2640 | 0.0860 | 0.1550 | 0.8060 | 0.734 | 0.3610 | 0.2990 | 0.747 | 0.8140 | 0.7730 | 0.665 | 0.4930 | 0.3270 | 0.871 | 0.6960 | 0.9960 | 0.6590 | 0.9960 | 0.0870 | 0.6410 | 0.6830 | 0.724 | 0.3740 | 0.1670 | 0.1030 | 0.9980 | 0.7930 | 0.4000 | 0.9460 | 0.4020 | 0.1030 | 0.5410 | 0.1850 | 0.5170 | 0.6720 | 0.9780 | 0.8570 | 0.3060 | 0.9260 | 0.3180 | 0.3350 | 0.7780 | 0.4250 | 0.9710 | 0.2280 | 0.322 | 0.2200 | 0.6760 | 0.6460 | 0.4340 | 0.5200 | 0.4450 | 0.9500 | 0.9610 | 0.1760 | 0.5830 | 0.9000 | 0.5220 | 0.5970 | 0.0720 | 0.1400 | 0.9980 | 0.9580 | 0.3400 | 0.3760 | 0.9620 | 0.4750 | 0.1690 | 0.8920 | 0.8210 | 0.936 | 0.6720 |
| GSEA | 0.006 | 0.0039 | 0.0081 | 0.0218 | 0.000 | 0.0079 | 0.0216 | 0.006 | 0.0157 | 0.0141 | 0.0426 | 0.022 | 0.002 | 0.0039 | 0.004 | 0.0139 | 0.0039 | 0.0194 | 0.0175 | 0.0041 | 0.0462 | 0.0182 | 0.0158 | 0.0189 | 0.0077 | 0.0142 | 0.0197 | 0.0155 | 0.048 | 0.0347 | 0.020 | 0.0038 | 0.0039 | 0.0374 | 0.0059 | 0.0277 | 0.0041 | 0.0077 | 0.0062 | 0.0436 | 0.0199 | 0.0122 | 0.0335 | 0.0201 | 0.0189 | 0.0266 | 0.0283 | 0.0261 | 0.0161 | 0.0101 | 0.025 | 0.0451 | 0.0137 | 0.0294 | 0.002 | 0.0317 | 0.0385 | 0.006 | 0.0356 | 0.0242 | 0.0356 | 0.0472 | 0.0121 | 0.0061 | 0.0079 | 0.0455 | 0.0062 | 0.0059 | 0.0139 | 0.035 | 0.0245 | 0.0019 | 0.0402 | 0.0179 | 0.0258 | 0.0101 | 0.0379 | 0.0472 | 0.0372 | 0.0277 | 0.0082 | 0.0292 | 0.0254 | 0.0409 | 0.0294 | 0.0371 | 0.0461 | 0.0329 | 0.0454 | 0.0296 | 0.0098 | 0.0126 | 0.0102 | 0.0041 | 0.006 | 0.0352 | 0.0388 | 0.0214 | 0.0057 | 0.0081 | 0.0099 | 0.0061 | 0.0202 | 0.0258 | 0.0344 | 0.0198 | 0.0459 | 0.0464 | 0.032 | 0.0386 | 0.0085 | 0.041 | 0.0081 | 0.0298 | 0.0484 | 0.0205 | 0.0176 | 0.0266 | 0.0484 | 0.014 | 0.0292 | 0.0188 | 0.0102 | 0.0431 | 0.0359 | 0.0475 | 0.0371 | 0.0385 | 0.012 | 0.0466 | 0.0216 | 0.0141 | 0.0041 | 0.0141 | 0.0281 | 0.0271 | 0.000 | 0.014 | 0.0222 | 0.0021 | 0.0211 | 0.0348 | 0.0346 | 0.0329 | 0.0198 | 0.045 | 0.0183 | 0.0423 | 0.0304 | 0.0202 | 0.0282 | 0.0377 | 0.0482 | 0.0103 | 0.0356 | 0.0426 | 0.0224 | 0.0266 | 0.0165 | 0.0285 | 0.0381 | 0.0217 | 0.0372 | 0.0316 | 0.0401 | 0.0311 | 0.0331 | 0.0375 | 0.0461 | 0.0319 | 0.0199 | 0.0402 | 0.0218 | 0.0275 | 0.0274 | 0.0338 | 0.0454 | 0.0276 | 0.039 | 0.0476 | 0.0188 | 0.0411 | 0.0344 | 0.0381 | 0.0402 | 0.0481 | 0.0225 | 0.0406 | 0.0364 | 0.048 | 0.0447 | 0.0379 | 0.0355 | 0.0478 | 0.0473 | 0.000 | 0.0037 | 0.0019 | 0.000 | 0.0078 | 0.0059 | 0.000 | 0.000 | 0.0113 | 0.0096 | 0.0038 | 0.0038 | 0.0038 | 0.0019 | 0.0038 | 0.000 | 0.0079 | 0.0152 | 0.0056 | 0.0201 | 0.0019 | 0.0353 | 0.0113 | 0.0242 | 0.0119 | 0.018 | 0.0057 | 0.0133 | 0.019 | 0.0321 | 0.0077 | 0.028 | 0.0249 | 0.0059 | 0.015 | 0.0078 | 0.0254 | 0.0156 | 0.0169 | 0.0114 | 0.0186 | 0.0252 | 0.019 | 0.0152 | 0.0333 | 0.0296 | 0.0019 | 0.0411 | 0.0209 | 0.0152 | 0.0111 | 0.0189 | 0.0248 | 0.0273 | 0.0252 | 0.0189 | 0.0099 | 0.0135 | 0.0328 | 0.0496 | 0.0361 | 0.0418 | 0.0421 | 0.0397 | 0.0365 | 0.0376 | 0.035 | 0.0291 | 0.0474 | 0.0342 | 0.0336 | 0.0382 | 0.0301 | 0.0411 | 0.0416 | 0.0342 | 0.0483 | 0.0262 | 0.0337 | 0.0361 | 0.0216 | 0.0412 | 0.0157 | 0.0437 | 0.0366 | 0.0473 | 0.0391 | 0.0366 | 0.0476 | 0.0218 | 0.0371 | 0.049 | 0.0301 |
# stopCluster(cl)
library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw())
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ABBUD_LIF_SIGNALING_1_DN"
## [1] "ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN"
## [1] "ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP"
## [1] "AIGNER_ZEB1_TARGETS"
## [1] "ALFANO_MYC_TARGETS"
## [1] "AMIT_SERUM_RESPONSE_240_MCF10A"
## [1] "AMIT_SERUM_RESPONSE_480_MCF10A"
## [1] "BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP"
## [1] "BAUS_TFF2_TARGETS_UP"
## [1] "BIOCARTA_PROTEASOME_PATHWAY"
## [1] "BOCHKIS_FOXA2_TARGETS"
## [1] "BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP"
## [1] "BROWNE_HCMV_INFECTION_1HR_DN"
## [1] "BROWNE_HCMV_INFECTION_48HR_UP"
## [1] "BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B"
## [1] "BURTON_ADIPOGENESIS_11"
## [1] "BURTON_ADIPOGENESIS_7"
## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN"
## [1] "CHANG_IMMORTALIZED_BY_HPV31_UP"
## [1] "CHENG_RESPONSE_TO_NICKEL_ACETATE"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN"
## [1] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"
## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"
## [1] "CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN"
## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP"
## [1] "DANG_MYC_TARGETS_DN"
## [1] "DAWSON_METHYLATED_IN_LYMPHOMA_TCL1"
## [1] "DE_YY1_TARGETS_DN"
## [1] "DELACROIX_RAR_BOUND_ES"
## [1] "DELLA_RESPONSE_TO_TSA_AND_BUTYRATE"
## [1] "DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP"
## [1] "DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN"
## [1] "DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN"
## [1] "EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION"
## [1] "FERRANDO_HOX11_NEIGHBORS"
## [1] "FUJII_YBX1_TARGETS_DN"
## [1] "GAVIN_FOXP3_TARGETS_CLUSTER_P2"
## [1] "GRADE_COLON_VS_RECTAL_CANCER_DN"
## [1] "GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN"
## [1] "GRESHOCK_CANCER_COPY_NUMBER_UP"
## [1] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"
## [1] "HECKER_IFNB1_TARGETS"
## [1] "HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP"
## [1] "HOELZEL_NF1_TARGETS_DN"
## [1] "HOLLERN_EMT_BREAST_TUMOR_DN"
## [1] "HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP"
## [1] "IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN"
## [1] "INGRAM_SHH_TARGETS_DN"
## [1] "ISSAEVA_MLL2_TARGETS"
## [1] "IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM"
## [1] "JAEGER_METASTASIS_UP"
## [1] "JI_METASTASIS_REPRESSED_BY_STK11"
## [1] "KAMMINGA_SENESCENCE"
## [1] "KEGG_PROTEASOME"
## [1] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"
## [1] "KUMAR_TARGETS_OF_MLL_AF9_FUSION"
## [1] "LABBE_WNT3A_TARGETS_DN"
## [1] "LEE_LIVER_CANCER_DENA_UP"
## [1] "LIAO_HAVE_SOX4_BINDING_SITES"
## [1] "LIU_SOX4_TARGETS_UP"
## [1] "LIU_VAV3_PROSTATE_CARCINOGENESIS_UP"
## [1] "LU_TUMOR_ANGIOGENESIS_UP"
## [1] "MAHADEVAN_IMATINIB_RESISTANCE_DN"
## [1] "MANN_RESPONSE_TO_AMIFOSTINE_UP"
## [1] "MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN"
## [1] "MARSON_FOXP3_TARGETS_STIMULATED_UP"
## [1] "MIKKELSEN_ES_ICP_WITH_H3K4ME3"
## [1] "MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"
## [1] "MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN"
## [1] "MORI_LARGE_PRE_BII_LYMPHOCYTE_DN"
## [1] "NEWMAN_ERCC6_TARGETS_UP"
## [1] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"
## [1] "NUTT_GBM_VS_AO_GLIOMA_UP"
## [1] "ONDER_CDH1_TARGETS_2_UP"
## [1] "ONO_AML1_TARGETS_DN"
## [1] "ONO_FOXP3_TARGETS_DN"
## [1] "OUYANG_PROSTATE_CANCER_PROGRESSION_DN"
## [1] "PASINI_SUZ12_TARGETS_UP"
## [1] "PENG_RAPAMYCIN_RESPONSE_UP"
## [1] "PETRETTO_CARDIAC_HYPERTROPHY"
## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"
## [1] "PID_HES_HEY_PATHWAY"
## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"
## [1] "POOLA_INVASIVE_BREAST_CANCER_UP"
## [1] "QI_PLASMACYTOMA_UP"
## [1] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"
## [1] "REACTOME_CHOLESTEROL_BIOSYNTHESIS"
## [1] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"
## [1] "REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES"
## [1] "REACTOME_DEVELOPMENTAL_BIOLOGY"
## [1] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"
## [1] "REACTOME_GPCR_DOWNSTREAM_SIGNALING"
## [1] "REACTOME_L1CAM_INTERACTIONS"
## [1] "REACTOME_MYOGENESIS"
## [1] "REACTOME_NEPHRIN_INTERACTIONS"
## [1] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"
## [1] "REACTOME_REGULATION_OF_SIGNALING_BY_CBL"
## [1] "REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE"
## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"
## [1] "RIZKI_TUMOR_INVASIVENESS_3D_UP"
## [1] "ROME_INSULIN_TARGETS_IN_MUSCLE_DN"
## [1] "RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN"
## [1] "ROY_WOUND_BLOOD_VESSEL_DN"
## [1] "SANSOM_APC_TARGETS_DN"
## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"
## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"
## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN"
## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP"
## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN"
## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"
## [1] "SIMBULAN_PARP1_TARGETS_DN"
## [1] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"
## [1] "SMID_BREAST_CANCER_LUMINAL_B_DN"
## [1] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"
## [1] "SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN"
## [1] "SMIRNOV_RESPONSE_TO_IR_6HR_DN"
## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN"
## [1] "THILLAINADESAN_ZNF217_TARGETS_UP"
## [1] "TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN"
## [1] "TSENG_ADIPOGENIC_POTENTIAL_UP"
## [1] "VANTVEER_BREAST_CANCER_BRCA1_UP"
## [1] "VECCHI_GASTRIC_CANCER_EARLY_DN"
## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_DN"
## [1] "WENDT_COHESIN_TARGETS_UP"
## [1] "WIELAND_UP_BY_HBV_INFECTION"
## [1] "WNT_SIGNALING"
## [1] "WONG_IFNA2_RESISTANCE_DN"
## [1] "WOO_LIVER_CANCER_RECURRENCE_UP"
## [1] "XU_CREBBP_TARGETS_DN"
## [1] "XU_GH1_AUTOCRINE_TARGETS_UP"
## [1] "YAGI_AML_WITH_11Q23_REARRANGED"
## [1] "YAMAZAKI_TCEB3_TARGETS_DN"
## [1] "YANG_BREAST_CANCER_ESR1_LASER_DN"
## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"
## [1] "ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP"
## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"
rownames(gsea_results_significant)
## [1] "HADDAD_B_LYMPHOCYTE_PROGENITOR"
## [2] "GOLUB_ALL_VS_AML_UP"
## [3] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"
## [4] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"
## [5] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN"
## [6] "KEGG_PRIMARY_IMMUNODEFICIENCY"
## [7] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"
## [8] "DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN"
## [9] "PUJANA_BRCA2_PCC_NETWORK"
## [10] "BILANGES_SERUM_SENSITIVE_VIA_TSC2"
## [11] "RAO_BOUND_BY_SALL4"
## [12] "KEGG_BASE_EXCISION_REPAIR"
## [13] "REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES"
## [14] "REACTOME_CELL_CYCLE"
## [15] "GARY_CD5_TARGETS_DN"
## [16] "MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6"
## [17] "DAZARD_RESPONSE_TO_UV_NHEK_DN"
## [18] "BENPORATH_PROLIFERATION"
## [19] "NUYTTEN_EZH2_TARGETS_DN"
## [20] "KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
## [21] "REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN"
## [22] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP"
## [23] "HUMMEL_BURKITTS_LYMPHOMA_UP"
## [24] "RAMALHO_STEMNESS_UP"
## [25] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"
## [26] "REACTOME_CELL_CYCLE_CHECKPOINTS"
## [27] "REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION"
## [28] "GENTILE_UV_RESPONSE_CLUSTER_D8"
## [29] "MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP"
## [30] "REACTOME_HIV_LIFE_CYCLE"
## [31] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP"
## [32] "REACTOME_HIV_INFECTION"
## [33] "REACTOME_CHROMOSOME_MAINTENANCE"
## [34] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"
## [35] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [36] "SIG_BCR_SIGNALING_PATHWAY"
## [37] "ZHANG_BREAST_CANCER_PROGENITORS_UP"
## [38] "PYEON_HPV_POSITIVE_TUMORS_UP"
## [39] "MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN"
## [40] "CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP"
## [41] "WANG_CLIM2_TARGETS_DN"
## [42] "MARSON_BOUND_BY_E2F4_UNSTIMULATED"
## [43] "SHEN_SMARCA2_TARGETS_UP"
## [44] "REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR"
## [45] "GRADE_METASTASIS_DN"
## [46] "REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY"
## [47] "REACTOME_BASE_EXCISION_REPAIR"
## [48] "REACTOME_CELL_CYCLE_MITOTIC"
## [49] "REACTOME_TRANSCRIPTION"
## [50] "KAUFFMANN_DNA_REPAIR_GENES"
## [51] "ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN"
## [52] "KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
## [53] "STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP"
## [54] "MITSIADES_RESPONSE_TO_APLIDIN_DN"
## [55] "REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS"
## [56] "BOYLAN_MULTIPLE_MYELOMA_C_D_UP"
## [57] "FEVR_CTNNB1_TARGETS_DN"
## [58] "REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY"
## [59] "REACTOME_TELOMERE_MAINTENANCE"
## [60] "BIDUS_METASTASIS_UP"
## [61] "ZHANG_TLX_TARGETS_36HR_DN"
## [62] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"
## [63] "HOLLMANN_APOPTOSIS_VIA_CD40_DN"
## [64] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL"
## [65] "KIM_WT1_TARGETS_DN"
## [66] "MORI_PLASMA_CELL_DN"
## [67] "ENK_UV_RESPONSE_KERATINOCYTE_DN"
## [68] "PID_BETA_CATENIN_NUC_PATHWAY"
## [69] "ZHAN_EARLY_DIFFERENTIATION_GENES_DN"
## [70] "REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS"
## [71] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP"
## [72] "MATTIOLI_MGUS_VS_PCL"
## [73] "ABRAMSON_INTERACT_WITH_AIRE"
## [74] "ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP"
## [75] "VILLANUEVA_LIVER_CANCER_KRT19_UP"
## [76] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"
## [77] "KEGG_SPLICEOSOME"
## [78] "MORI_MATURE_B_LYMPHOCYTE_DN"
## [79] "DITTMER_PTHLH_TARGETS_DN"
## [80] "CAIRO_HEPATOBLASTOMA_UP"
## [81] "BIOCARTA_BCR_PATHWAY"
## [82] "BASSO_CD40_SIGNALING_DN"
## [83] "REACTOME_MRNA_PROCESSING"
## [84] "HAMAI_APOPTOSIS_VIA_TRAIL_UP"
## [85] "ROSS_AML_WITH_AML1_ETO_FUSION"
## [86] "REACTOME_GLUCOSE_TRANSPORT"
## [87] "REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1"
## [88] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"
## [89] "PECE_MAMMARY_STEM_CELL_DN"
## [90] "DAZARD_UV_RESPONSE_CLUSTER_G6"
## [91] "SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES"
## [92] "GENTILE_UV_RESPONSE_CLUSTER_D4"
## [93] "REACTOME_METABOLISM_OF_NON_CODING_RNA"
## [94] "CHESLER_BRAIN_QTL_CIS"
## [95] "REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE"
## [96] "KAMMINGA_EZH2_TARGETS"
## [97] "JOHNSTONE_PARVB_TARGETS_3_DN"
## [98] "CROMER_METASTASIS_UP"
## [99] "HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2"
## [100] "BROWNE_HCMV_INFECTION_10HR_DN"
## [101] "PEART_HDAC_PROLIFERATION_CLUSTER_UP"
## [102] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"
## [103] "REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE"
## [104] "GALE_APL_WITH_FLT3_MUTATED_UP"
## [105] "REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C"
## [106] "HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN"
## [107] "PROVENZANI_METASTASIS_UP"
## [108] "HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC"
## [109] "KLEIN_TARGETS_OF_BCR_ABL1_FUSION"
## [110] "BIOCARTA_CARM_ER_PATHWAY"
## [111] "REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION"
## [112] "VALK_AML_CLUSTER_10"
## [113] "MILI_PSEUDOPODIA_HAPTOTAXIS_UP"
## [114] "HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP"
## [115] "BIOCARTA_PAR1_PATHWAY"
## [116] "SESTO_RESPONSE_TO_UV_C2"
## [117] "CARD_MIR302A_TARGETS"
## [118] "REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1"
## [119] "REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1"
## [120] "REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION"
## [121] "ELLWOOD_MYC_TARGETS_DN"
## [122] "PID_BCR_5PATHWAY"
## [123] "BENPORATH_SOX2_TARGETS"
## [124] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS"
## [125] "BROWNE_HCMV_INFECTION_4HR_DN"
## [126] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"
## [127] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP"
## [128] "WAKASUGI_HAVE_ZNF143_BINDING_SITES"
## [129] "KIM_ALL_DISORDERS_CALB1_CORR_UP"
## [130] "ROESSLER_LIVER_CANCER_METASTASIS_DN"
## [131] "REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT"
## [132] "REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT"
## [133] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"
## [134] "BENPORATH_ES_1"
## [135] "PID_EPHA2_FWD_PATHWAY"
## [136] "REACTOME_RNA_POL_I_TRANSCRIPTION"
## [137] "YANG_BREAST_CANCER_ESR1_DN"
## [138] "REACTOME_MEIOSIS"
## [139] "REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC"
## [140] "ST_B_CELL_ANTIGEN_RECEPTOR"
## [141] "BOYLAN_MULTIPLE_MYELOMA_C_UP"
## [142] "VALK_AML_CLUSTER_1"
## [143] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
## [144] "HOLLMANN_APOPTOSIS_VIA_CD40_UP"
## [145] "WHITFIELD_CELL_CYCLE_G2_M"
## [146] "BRUINS_UVC_RESPONSE_MIDDLE"
## [147] "NOUZOVA_TRETINOIN_AND_H4_ACETYLATION"
## [148] "LEE_RECENT_THYMIC_EMIGRANT"
## [149] "PID_P38_MK2_PATHWAY"
## [150] "KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP"
## [151] "CHENG_IMPRINTED_BY_ESTRADIOL"
## [152] "GAZIN_EPIGENETIC_SILENCING_BY_KRAS"
## [153] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"
## [154] "TIEN_INTESTINE_PROBIOTICS_2HR_DN"
## [155] "ZUCCHI_METASTASIS_UP"
## [156] "PID_P53_REGULATION_PATHWAY"
## [157] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS"
## [158] "REACTOME_PI_METABOLISM"
## [159] "PARK_HSC_AND_MULTIPOTENT_PROGENITORS"
## [160] "BAKKER_FOXO3_TARGETS_DN"
## [161] "REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS"
## [162] "KIM_GERMINAL_CENTER_T_HELPER_UP"
## [163] "PID_PS1_PATHWAY"
## [164] "OUILLETTE_CLL_13Q14_DELETION_UP"
## [165] "THUM_SYSTOLIC_HEART_FAILURE_DN"
## [166] "REACTOME_APOPTOSIS"
## [167] "ZHAN_MULTIPLE_MYELOMA_PR_DN"
## [168] "SESTO_RESPONSE_TO_UV_C5"
## [169] "PID_AR_NONGENOMIC_PATHWAY"
## [170] "ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP"
## [171] "JI_RESPONSE_TO_FSH_UP"
## [172] "BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP"
## [173] "SIG_CHEMOTAXIS"
## [174] "BRUINS_UVC_RESPONSE_EARLY_LATE"
## [175] "LIN_MELANOMA_COPY_NUMBER_DN"
## [176] "REACTOME_ADAPTIVE_IMMUNE_SYSTEM"
## [177] "BIOCARTA_CTCF_PATHWAY"
## [178] "JOHNSTONE_PARVB_TARGETS_2_DN"
## [179] "ACEVEDO_LIVER_CANCER_UP"
## [180] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP"
## [181] "LAIHO_COLORECTAL_CANCER_SERRATED_DN"
## [182] "RIZKI_TUMOR_INVASIVENESS_2D_UP"
## [183] "CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE"
## [184] "PID_HEDGEHOG_GLI_PATHWAY"
## [185] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"
## [186] "LIN_MELANOMA_COPY_NUMBER_UP"
## [187] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"
## [188] "HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP"
## [189] "BIOCARTA_TFF_PATHWAY"
## [190] "HOSHIDA_LIVER_CANCER_SUBCLASS_S2"
## [191] "BENPORATH_OCT4_TARGETS"
## [192] "GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP"
## [193] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"
## [194] "SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP"
## [195] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"
## [196] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"
## [197] "BILD_E2F3_ONCOGENIC_SIGNATURE"
## [198] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"
## [199] "WOOD_EBV_EBNA1_TARGETS_DN"
## [200] "BOYLAN_MULTIPLE_MYELOMA_PCA3_DN"
## [201] "BENPORATH_NANOG_TARGETS"
## [202] "WINTER_HYPOXIA_DN"
## [203] "IKEDA_MIR30_TARGETS_UP"
## [204] "REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK"
## [205] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD"
## [206] "HASLINGER_B_CLL_WITH_6Q21_DELETION"
## [207] "BIOCARTA_WNT_PATHWAY"
## [208] "YAGI_AML_WITH_T_9_11_TRANSLOCATION"
## [209] "HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN"
## [210] "BIOCARTA_CXCR4_PATHWAY"
## [211] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"
## [212] "GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP"
## [213] "ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN"
## [214] "ZHAN_MULTIPLE_MYELOMA_HP_UP"
## [215] "REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION"
## [216] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN"
## [217] "VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP"
## [218] "ONKEN_UVEAL_MELANOMA_UP"
## [219] "BILBAN_B_CLL_LPL_UP"
## [220] "CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS"
## [221] "KEGG_NOTCH_SIGNALING_PATHWAY"
## [222] "HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP"
## [223] "LEE_CALORIE_RESTRICTION_MUSCLE_DN"
## [224] "BAELDE_DIABETIC_NEPHROPATHY_DN"
## [225] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"
## [226] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
## [227] "KATSANOU_ELAVL1_TARGETS_DN"
## [228] "LABBE_WNT3A_TARGETS_UP"
## [229] "GYORFFY_MITOXANTRONE_RESISTANCE"
## [230] "MULLIGHAN_NPM1_SIGNATURE_3_DN"
## [231] "JIANG_TIP30_TARGETS_UP"
## [232] "REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS"
## [233] "GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN"
## [234] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2"
## [235] "HOSHIDA_LIVER_CANCER_SURVIVAL_UP"
## [236] "BHAT_ESR1_TARGETS_VIA_AKT1_DN"
## [237] "HOFMANN_CELL_LYMPHOMA_UP"
## [238] "STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP"
## [239] "ABBUD_LIF_SIGNALING_1_UP"
## [240] "DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS"
## [241] "CHEOK_RESPONSE_TO_HD_MTX_UP"
## [242] "REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS"
## [243] "VERHAAK_AML_WITH_NPM1_MUTATED_UP"
## [244] "PID_INTEGRIN_CS_PATHWAY"
## [245] "PID_UPA_UPAR_PATHWAY"
## [246] "REACTOME_COLLAGEN_FORMATION"
## [247] "DALESSIO_TSA_RESPONSE"
## [248] "GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN"
## [249] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"
## [250] "BIOCARTA_DC_PATHWAY"
## [251] "NAKAJIMA_MAST_CELL"
## [252] "REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE"
## [253] "KIM_ALL_DISORDERS_CALB1_CORR_DN"
## [254] "GOLUB_ALL_VS_AML_DN"
## [255] "PID_INTEGRIN2_PATHWAY"
## [256] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"
## [257] "LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS"
## [258] "KRIEG_HYPOXIA_VIA_KDM3A"
## [259] "LEE_LIVER_CANCER_E2F1_UP"
## [260] "PID_SYNDECAN_1_PATHWAY"
## [261] "PARK_APL_PATHOGENESIS_DN"
## [262] "HWANG_PROSTATE_CANCER_MARKERS"
## [263] "ALONSO_METASTASIS_NEURAL_UP"
## [264] "AMIT_EGF_RESPONSE_120_MCF10A"
## [265] "LI_CISPLATIN_RESISTANCE_DN"
## [266] "REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL"
## [267] "VERRECCHIA_RESPONSE_TO_TGFB1_C2"
## [268] "GROSS_ELK3_TARGETS_DN"
## [269] "ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION"
## [270] "NABA_COLLAGENS"
## [271] "GHANDHI_BYSTANDER_IRRADIATION_UP"
## [272] "KOHOUTEK_CCNT1_TARGETS"
## [273] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN"
## [274] "KOBAYASHI_EGFR_SIGNALING_6HR_DN"
## [275] "REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS"
## [276] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"
## [277] "SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP"
## [278] "REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION"
## [279] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"
## [280] "VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP"
## [281] "BROWN_MYELOID_CELL_DEVELOPMENT_UP"
## [282] "KEGG_ARACHIDONIC_ACID_METABOLISM"
## [283] "KANG_AR_TARGETS_UP"
## [284] "ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP"
## [285] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP"
## [286] "HOLLERN_MICROACINAR_BREAST_TUMOR_UP"
## [287] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN"
## [288] "MIKKELSEN_MEF_ICP_WITH_H3K27ME3"
## [289] "GHANDHI_DIRECT_IRRADIATION_UP"
## [290] "BIOCARTA_CYTOKINE_PATHWAY"
## [291] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"
## [292] "YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP"
## [293] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"
## [294] "PID_RXR_VDR_PATHWAY"
## [295] "XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR"
## [296] "WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG"
## [297] "KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
## [298] "HUPER_BREAST_BASAL_VS_LUMINAL_UP"
## [299] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"
## [300] "JEON_SMAD6_TARGETS_UP"
## [301] "PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP"
## [302] "PID_INTEGRIN5_PATHWAY"
## [303] "BIOCARTA_STEM_PATHWAY"
## [304] "NAKAMURA_ADIPOGENESIS_EARLY_UP"
## [305] "BIOCARTA_INFLAM_PATHWAY"
## [306] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"
## [307] "REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS"
## [308] "KHETCHOUMIAN_TRIM24_TARGETS_UP"
## [309] "NAKAJIMA_EOSINOPHIL"
## [310] "SEMENZA_HIF1_TARGETS"
## [311] "MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP"
## [312] "AMIT_EGF_RESPONSE_120_HELA"
## [313] "YANG_MUC2_TARGETS_DUODENUM_6MO_DN"
## [314] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"
## [315] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"
## [316] "SABATES_COLORECTAL_ADENOMA_UP"
## [317] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN"
## [318] "SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A"
## [319] "MADAN_DPPA4_TARGETS"
## [320] "URS_ADIPOCYTE_DIFFERENTIATION_UP"
## [321] "ONDER_CDH1_SIGNALING_VIA_CTNNB1"
## [322] "KERLEY_RESPONSE_TO_CISPLATIN_UP"
## [323] "CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP"
## [324] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"
## [325] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN"
## [326] "SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN"
## [327] "MARKEY_RB1_CHRONIC_LOF_DN"
## [328] "SHEN_SMARCA2_TARGETS_DN"
## [329] "NABA_ECM_AFFILIATED"
## [330] "KIM_LIVER_CANCER_POOR_SURVIVAL_DN"
## [331] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"
## [332] "MARTENS_TRETINOIN_RESPONSE_UP"
## [333] "WATANABE_COLON_CANCER_MSI_VS_MSS_UP"
## [334] "MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP"
## [335] "REACTOME_GPCR_LIGAND_BINDING"
for (name in (Significant_in_GSEA_not_in_dcor)){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name"))
# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN"
## [1] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"
## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN"
## [1] "PUJANA_BRCA2_PCC_NETWORK"
## [1] "KEGG_BASE_EXCISION_REPAIR"
## [1] "REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES"
## [1] "REACTOME_CELL_CYCLE"
## [1] "GARY_CD5_TARGETS_DN"
## [1] "MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6"
## [1] "DAZARD_RESPONSE_TO_UV_NHEK_DN"
## [1] "BENPORATH_PROLIFERATION"
## [1] "NUYTTEN_EZH2_TARGETS_DN"
## [1] "KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY"
## [1] "REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN"
## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP"
## [1] "RAMALHO_STEMNESS_UP"
## [1] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"
## [1] "REACTOME_CELL_CYCLE_CHECKPOINTS"
## [1] "REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION"
## [1] "GENTILE_UV_RESPONSE_CLUSTER_D8"
## [1] "MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP"
## [1] "REACTOME_HIV_LIFE_CYCLE"
## [1] "REACTOME_HIV_INFECTION"
## [1] "REACTOME_CHROMOSOME_MAINTENANCE"
## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"
## [1] "ZHANG_BREAST_CANCER_PROGENITORS_UP"
## [1] "PYEON_HPV_POSITIVE_TUMORS_UP"
## [1] "MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN"
## [1] "CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP"
## [1] "MARSON_BOUND_BY_E2F4_UNSTIMULATED"
## [1] "SHEN_SMARCA2_TARGETS_UP"
## [1] "REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY"
## [1] "REACTOME_BASE_EXCISION_REPAIR"
## [1] "REACTOME_CELL_CYCLE_MITOTIC"
## [1] "REACTOME_TRANSCRIPTION"
## [1] "KAUFFMANN_DNA_REPAIR_GENES"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN"
## [1] "KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION"
## [1] "STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP"
## [1] "MITSIADES_RESPONSE_TO_APLIDIN_DN"
## [1] "REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS"
## [1] "BOYLAN_MULTIPLE_MYELOMA_C_D_UP"
## [1] "FEVR_CTNNB1_TARGETS_DN"
## [1] "REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY"
## [1] "REACTOME_TELOMERE_MAINTENANCE"
## [1] "BIDUS_METASTASIS_UP"
## [1] "ZHANG_TLX_TARGETS_36HR_DN"
## [1] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"
## [1] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL"
## [1] "KIM_WT1_TARGETS_DN"
## [1] "MORI_PLASMA_CELL_DN"
## [1] "ENK_UV_RESPONSE_KERATINOCYTE_DN"
## [1] "ZHAN_EARLY_DIFFERENTIATION_GENES_DN"
## [1] "REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS"
## [1] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP"
## [1] "MATTIOLI_MGUS_VS_PCL"
## [1] "ABRAMSON_INTERACT_WITH_AIRE"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP"
## [1] "VILLANUEVA_LIVER_CANCER_KRT19_UP"
## [1] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"
## [1] "KEGG_SPLICEOSOME"
## [1] "MORI_MATURE_B_LYMPHOCYTE_DN"
## [1] "DITTMER_PTHLH_TARGETS_DN"
## [1] "CAIRO_HEPATOBLASTOMA_UP"
## [1] "BIOCARTA_BCR_PATHWAY"
## [1] "REACTOME_MRNA_PROCESSING"
## [1] "HAMAI_APOPTOSIS_VIA_TRAIL_UP"
## [1] "ROSS_AML_WITH_AML1_ETO_FUSION"
## [1] "REACTOME_GLUCOSE_TRANSPORT"
## [1] "REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1"
## [1] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"
## [1] "PECE_MAMMARY_STEM_CELL_DN"
## [1] "DAZARD_UV_RESPONSE_CLUSTER_G6"
## [1] "GENTILE_UV_RESPONSE_CLUSTER_D4"
## [1] "REACTOME_METABOLISM_OF_NON_CODING_RNA"
## [1] "CHESLER_BRAIN_QTL_CIS"
## [1] "REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE"
## [1] "KAMMINGA_EZH2_TARGETS"
## [1] "JOHNSTONE_PARVB_TARGETS_3_DN"
## [1] "HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2"
## [1] "BROWNE_HCMV_INFECTION_10HR_DN"
## [1] "PEART_HDAC_PROLIFERATION_CLUSTER_UP"
## [1] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"
## [1] "REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE"
## [1] "GALE_APL_WITH_FLT3_MUTATED_UP"
## [1] "REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C"
## [1] "HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN"
## [1] "HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC"
## [1] "BIOCARTA_CARM_ER_PATHWAY"
## [1] "REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION"
## [1] "VALK_AML_CLUSTER_10"
## [1] "MILI_PSEUDOPODIA_HAPTOTAXIS_UP"
## [1] "BIOCARTA_PAR1_PATHWAY"
## [1] "SESTO_RESPONSE_TO_UV_C2"
## [1] "CARD_MIR302A_TARGETS"
## [1] "REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1"
## [1] "REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1"
## [1] "REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION"
## [1] "ELLWOOD_MYC_TARGETS_DN"
## [1] "BENPORATH_SOX2_TARGETS"
## [1] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS"
## [1] "BROWNE_HCMV_INFECTION_4HR_DN"
## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP"
## [1] "WAKASUGI_HAVE_ZNF143_BINDING_SITES"
## [1] "KIM_ALL_DISORDERS_CALB1_CORR_UP"
## [1] "ROESSLER_LIVER_CANCER_METASTASIS_DN"
## [1] "REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT"
## [1] "REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT"
## [1] "REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION"
## [1] "BENPORATH_ES_1"
## [1] "PID_EPHA2_FWD_PATHWAY"
## [1] "REACTOME_RNA_POL_I_TRANSCRIPTION"
## [1] "YANG_BREAST_CANCER_ESR1_DN"
## [1] "REACTOME_MEIOSIS"
## [1] "REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC"
## [1] "BOYLAN_MULTIPLE_MYELOMA_C_UP"
## [1] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"
## [1] "HOLLMANN_APOPTOSIS_VIA_CD40_UP"
## [1] "WHITFIELD_CELL_CYCLE_G2_M"
## [1] "BRUINS_UVC_RESPONSE_MIDDLE"
## [1] "PID_P38_MK2_PATHWAY"
## [1] "KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP"
## [1] "CHENG_IMPRINTED_BY_ESTRADIOL"
## [1] "GAZIN_EPIGENETIC_SILENCING_BY_KRAS"
## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"
## [1] "TIEN_INTESTINE_PROBIOTICS_2HR_DN"
## [1] "ZUCCHI_METASTASIS_UP"
## [1] "PID_P53_REGULATION_PATHWAY"
## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS"
## [1] "REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS"
## [1] "KIM_GERMINAL_CENTER_T_HELPER_UP"
## [1] "PID_PS1_PATHWAY"
## [1] "OUILLETTE_CLL_13Q14_DELETION_UP"
## [1] "THUM_SYSTOLIC_HEART_FAILURE_DN"
## [1] "REACTOME_APOPTOSIS"
## [1] "PID_AR_NONGENOMIC_PATHWAY"
## [1] "ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP"
## [1] "JI_RESPONSE_TO_FSH_UP"
## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP"
## [1] "SIG_CHEMOTAXIS"
## [1] "BRUINS_UVC_RESPONSE_EARLY_LATE"
## [1] "LIN_MELANOMA_COPY_NUMBER_DN"
## [1] "JOHNSTONE_PARVB_TARGETS_2_DN"
## [1] "ACEVEDO_LIVER_CANCER_UP"
## [1] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP"
## [1] "LAIHO_COLORECTAL_CANCER_SERRATED_DN"
## [1] "PID_HEDGEHOG_GLI_PATHWAY"
## [1] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"
## [1] "LIN_MELANOMA_COPY_NUMBER_UP"
## [1] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"
## [1] "HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP"
## [1] "BIOCARTA_TFF_PATHWAY"
## [1] "HOSHIDA_LIVER_CANCER_SUBCLASS_S2"
## [1] "BENPORATH_OCT4_TARGETS"
## [1] "GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP"
## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"
## [1] "SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP"
## [1] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"
## [1] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"
## [1] "BILD_E2F3_ONCOGENIC_SIGNATURE"
## [1] "LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN"
## [1] "WOOD_EBV_EBNA1_TARGETS_DN"
## [1] "BENPORATH_NANOG_TARGETS"
## [1] "WINTER_HYPOXIA_DN"
## [1] "IKEDA_MIR30_TARGETS_UP"
## [1] "REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK"
## [1] "KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD"
## [1] "HASLINGER_B_CLL_WITH_6Q21_DELETION"
## [1] "BIOCARTA_WNT_PATHWAY"
## [1] "YAGI_AML_WITH_T_9_11_TRANSLOCATION"
## [1] "HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN"
## [1] "BIOCARTA_CXCR4_PATHWAY"
## [1] "TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA"
## [1] "GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP"
## [1] "ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN"
## [1] "ZHAN_MULTIPLE_MYELOMA_HP_UP"
## [1] "REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION"
## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN"
## [1] "VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP"
## [1] "BILBAN_B_CLL_LPL_UP"
## [1] "CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS"
## [1] "KEGG_NOTCH_SIGNALING_PATHWAY"
## [1] "HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP"
## [1] "LEE_CALORIE_RESTRICTION_MUSCLE_DN"
## [1] "KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION"
## [1] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"
## [1] "KATSANOU_ELAVL1_TARGETS_DN"
## [1] "GYORFFY_MITOXANTRONE_RESISTANCE"
## [1] "MULLIGHAN_NPM1_SIGNATURE_3_DN"
## [1] "JIANG_TIP30_TARGETS_UP"
## [1] "REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS"
## [1] "GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN"
## [1] "CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2"
## [1] "HOFMANN_CELL_LYMPHOMA_UP"
## [1] "STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP"
## [1] "ABBUD_LIF_SIGNALING_1_UP"
## [1] "DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS"
## [1] "CHEOK_RESPONSE_TO_HD_MTX_UP"
## [1] "REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS"
## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_UP"
## [1] "PID_INTEGRIN_CS_PATHWAY"
## [1] "PID_UPA_UPAR_PATHWAY"
## [1] "REACTOME_COLLAGEN_FORMATION"
## [1] "DALESSIO_TSA_RESPONSE"
## [1] "GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN"
## [1] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"
## [1] "BIOCARTA_DC_PATHWAY"
## [1] "NAKAJIMA_MAST_CELL"
## [1] "REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE"
## [1] "KIM_ALL_DISORDERS_CALB1_CORR_DN"
## [1] "GOLUB_ALL_VS_AML_DN"
## [1] "PID_INTEGRIN2_PATHWAY"
## [1] "HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN"
## [1] "LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS"
## [1] "KRIEG_HYPOXIA_VIA_KDM3A"
## [1] "PID_SYNDECAN_1_PATHWAY"
## [1] "PARK_APL_PATHOGENESIS_DN"
## [1] "HWANG_PROSTATE_CANCER_MARKERS"
## [1] "ALONSO_METASTASIS_NEURAL_UP"
## [1] "AMIT_EGF_RESPONSE_120_MCF10A"
## [1] "LI_CISPLATIN_RESISTANCE_DN"
## [1] "REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL"
## [1] "VERRECCHIA_RESPONSE_TO_TGFB1_C2"
## [1] "GROSS_ELK3_TARGETS_DN"
## [1] "ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION"
## [1] "NABA_COLLAGENS"
## [1] "GHANDHI_BYSTANDER_IRRADIATION_UP"
## [1] "KOHOUTEK_CCNT1_TARGETS"
## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN"
## [1] "KOBAYASHI_EGFR_SIGNALING_6HR_DN"
## [1] "REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS"
## [1] "SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP"
## [1] "REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION"
## [1] "MIKKELSEN_MCV6_ICP_WITH_H3K27ME3"
## [1] "VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP"
## [1] "KEGG_ARACHIDONIC_ACID_METABOLISM"
## [1] "KANG_AR_TARGETS_UP"
## [1] "ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP"
## [1] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP"
## [1] "HOLLERN_MICROACINAR_BREAST_TUMOR_UP"
## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN"
## [1] "MIKKELSEN_MEF_ICP_WITH_H3K27ME3"
## [1] "GHANDHI_DIRECT_IRRADIATION_UP"
## [1] "BIOCARTA_CYTOKINE_PATHWAY"
## [1] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"
## [1] "YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP"
## [1] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"
## [1] "PID_RXR_VDR_PATHWAY"
## [1] "XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR"
## [1] "WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG"
## [1] "KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES"
## [1] "HUPER_BREAST_BASAL_VS_LUMINAL_UP"
## [1] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"
## [1] "JEON_SMAD6_TARGETS_UP"
## [1] "PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP"
## [1] "PID_INTEGRIN5_PATHWAY"
## [1] "BIOCARTA_STEM_PATHWAY"
## [1] "NAKAMURA_ADIPOGENESIS_EARLY_UP"
## [1] "BIOCARTA_INFLAM_PATHWAY"
## [1] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"
## [1] "REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS"
## [1] "KHETCHOUMIAN_TRIM24_TARGETS_UP"
## [1] "NAKAJIMA_EOSINOPHIL"
## [1] "SEMENZA_HIF1_TARGETS"
## [1] "MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP"
## [1] "AMIT_EGF_RESPONSE_120_HELA"
## [1] "YANG_MUC2_TARGETS_DUODENUM_6MO_DN"
## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_5_DN"
## [1] "REACTOME_AMINE_LIGAND_BINDING_RECEPTORS"
## [1] "SABATES_COLORECTAL_ADENOMA_UP"
## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN"
## [1] "SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A"
## [1] "MADAN_DPPA4_TARGETS"
## [1] "URS_ADIPOCYTE_DIFFERENTIATION_UP"
## [1] "ONDER_CDH1_SIGNALING_VIA_CTNNB1"
## [1] "KERLEY_RESPONSE_TO_CISPLATIN_UP"
## [1] "CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP"
## [1] "MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3"
## [1] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN"
## [1] "SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN"
## [1] "MARKEY_RB1_CHRONIC_LOF_DN"
## [1] "SHEN_SMARCA2_TARGETS_DN"
## [1] "NABA_ECM_AFFILIATED"
## [1] "KIM_LIVER_CANCER_POOR_SURVIVAL_DN"
## [1] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"
## [1] "MARTENS_TRETINOIN_RESPONSE_UP"
## [1] "WATANABE_COLON_CANCER_MSI_VS_MSS_UP"
## [1] "MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP"